Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi1g61 . . . . . . . . . . . . . . . Cpe09g00214 . . . . . . . . Cla05g02401 Cam05g2577 Cec05g2611 Cco05g2649 Clacu05g2580 Cmu05g2434 Cre05g2551 Cone13ag0915 Cone19ag0911 . . Lsi04g00371 . . Cme10g00367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g62 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g63 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g64 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g65 . Blo16g01091 . Bda11g01182 Bpe13g01380 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bda11g01182 . Bpe02g02319 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g66 . . Bda01g02130 . . . Bma14g01641 . . Cmo18g01134 . Cma18g01112 . Car18g01026 Sed06g1770 . . Bhi07g01503 Tan04g1016 Cmetu03g1484 . . . . . . . . . . . . . . . . Csa05g02505 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g67 . . . . . . . . . . . . . . . . . Bhi07g01504 . . Lac13g0368 Hepe10g1789 . . . . . . . . . . . . . . Csa05g02504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g68 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g69 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g70 . . . . . Bpe10g00894 . Bma15g00136 Cmo04g01772 . . . . . Sed07g1998 . Cpe01g01496 Bhi07g01513 Tan04g1024 Cmetu10g0886 Lac13g0362 Hepe10g1783 . . Cla05g02405 Cam05g2582 Cec05g2614 Cco05g2654 Clacu05g2584 Cmu05g2438 Cre05g2555 . . . . Lsi04g00375 Csa05g02498 Chy10g01047 Cme10g00373 Blo06g00925 . . . . . . . . . . Cma04g01691 . Car04g01727 . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 57297671 57301150 - Bda004461.1 Bda01g02130 2130
11 12200420 12201328 - Bda007680.1 Bda11g01182 1182
7 43601106 43606764 - XM_039036477.1 Bhi07g01503 1503
7 43601106 43606409 - XM_039036478.1 Bhi07g01504 1504
7 43769499 43772705 + XM_039037386.1 Bhi07g01513 1513
6 32479898 32487504 - BLOR17508 Blo06g00925 925
16 39422069 39426403 - BLOR21878 Blo16g01091 1091
14 34709065 34711762 - Bma012356.1 Bma14g01641 1641
15 1463102 1465760 + Bma013115.2 Bma15g00136 136
2 23836113 23839048 - Bpe010135.1 Bpe02g02319 2319
10 14656052 14658594 - Bpe003198.1 Bpe10g00894 894
13 19035024 19035932 - Bpe011040.1 Bpe13g01380 1380
5 33479181 33485577 - CaPI482276_05g025770.1 Cam05g2577 2577
5 33501320 33504626 + CaPI482276_05g025820.1 Cam05g2582 2582
4 9902349 9907292 - Carg14378-RA Car04g01727 1727
18 10626536 10630932 - Carg17304-RA Car18g01026 1026
5 34594322 34600720 - CcPI632755_05g026490.1 Cco05g2649 2649
5 34616226 34619564 + CcPI632755_05g026540.1 Cco05g2654 2654
5 36923092 36929479 - CePI673135_05g026110.1 Cec05g2611 2611
5 36940426 36948315 + CePI673135_05g026140.1 Cec05g2614 2614
10 15692996 15699845 - Chy10G182410.1 Chy10g01047 1047
5 33687268 33693625 - ClG42_05g0258000.10 Clacu05g2580 2580
5 33708975 33712196 + ClG42_05g0258400.10 Clacu05g2584 2584
5 35560332 35566533 - ClCG05G023800.2 Cla05g02401 2401
5 35582311 35585532 + ClCG05G023840.1 Cla05g02405 2405
4 8505698 8508186 - CmaCh04G016910.1 Cma04g01691 1691
18 9060991 9064124 - CmaCh18G011120.1 Cma18g01112 1112
10 2356012 2362148 - MELO3C012142.2.1 Cme10g00367 367
10 2392180 2394438 + MELO3C012138.2.1 Cme10g00373 373
3 5630260 5633311 - PI0023092.1 Cmetu03g1484 1484
10 19628034 19630371 - PI0000873.1 Cmetu10g0886 886
4 8939870 8942782 - CmoCh04G017720.1 Cmo04g01772 1772
18 11638090 11642472 - CmoCh18G011340.1 Cmo18g01134 1134
5 33425068 33431425 - CmPI595203_05g024340.1 Cmu05g2434 2434
5 33446755 33449974 + CmPI595203_05g024380.1 Cmu05g2438 2438
13 8029330 8033464 - Conep13aG0094300.1 Cone13ag0915 915
19 7083211 7084940 - Conep19aG0093700.1 Cone19ag0911 911
1 8929471 8933150 - Cp4.1LG01g12260.1 Cpe01g01496 1496
9 1229204 1235929 + Cp4.1LG09g02060.1 Cpe09g00214 214
5 36777770 36784161 - CrPI670011_05g025510.1 Cre05g2551 2551
5 36795402 36803248 + CrPI670011_05g025550.1 Cre05g2555 2555
5 26637691 26642035 - CsaV3_5G033170.1 Csa05g02498 2498
5 26670609 26672677 + CsaV3_5G033230.1 Csa05g02504 2504
5 26672739 26674074 + CsaV3_5G033240.1 Csa05g02505 2505
10 54589510 54593147 - Hsped.10g17830.1 Hepe10g1783 1783
10 54643940 54647684 + Hsped.10g17890.1 Hepe10g1789 1789
13 2580961 2583292 - Lag0040158.1 Lac13g0362 362
13 2611182 2614828 + Lag0040164.1 Lac13g0368 368
4 3696582 3707691 - Lsi04G003710.1 Lsi04g00371 371
4 3720243 3721912 + Lsi04G003750.1 Lsi04g00375 375
6 42429129 42434212 + Sed0019559.1 Sed06g1770 1770
7 34910440 34912693 + Sed0016842.1 Sed07g1998 1998
4 9041783 9045531 - Tan0008259.1 Tan04g1016 1016
4 9103686 9105982 + Tan0017520.1 Tan04g1024 1024
1 649076 654363 - Vvi1g61 Vvi1g61 61
1 656269 666920 + Vvi1g62 Vvi1g62 62
1 667766 679204 - Vvi1g63 Vvi1g63 63
1 679482 685333 - Vvi1g64 Vvi1g64 64
1 688227 696254 + Vvi1g65 Vvi1g65 65
1 697862 701409 - Vvi1g66 Vvi1g66 66
1 701418 707690 - Vvi1g67 Vvi1g67 67
1 710555 714160 - Vvi1g68 Vvi1g68 68
1 715658 718644 - Vvi1g69 Vvi1g69 69
1 721720 725418 + Vvi1g70 Vvi1g70 70
       

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